We are interested in finding the R/S (R=replacement, S= silent)
ratio of somatic point mutations in the immunoglobulin variable
region genes. This is done by aligning the DNA sequence of the
mutated gene to its germline counterpart defining its mutations,
and determining their type (replacement or silent mutation).
This is done by translating the sequence into a protein and
comparing it to the translation of the germline sequence.
(A silent mutation in the DNA will produce the same amino acid
as is in the germline, while a replacement mutation will give rise to a
different amino acid.)
Since the random mutation frequency differs for each of the 4 DNA
nucleotide bases, one has to introduce these frequencies into the
calculation to obtain the expected R/S value for the studied gene.
These calculations which lead to determination of the R/S values due to
random mutations, could then be compared with the actual R/S ratio and
large divergence from the expected random R/S value would suggest that a
positive or negative selection process is taking place.
I would like to know whether there is an available computer program to
calculate the random R/S ratio, and from whom it can be obtained.
I would appreciate if anyone could point me in the right direction
and please, Cc: to me by e-mail
chana_g at gene.md.huji.ac.il
as well as to newsgroups.
Thanks in advance, Chana Gabay